************************************************** * * * 1.0系列新闻 * * * ************************************************** 阿GENOMINATOR 1.1版本新特性的变化包括一个例子在装饰图案与启动权重以及部分基因模型。o增加了computePrimingWeights和addPrimingWeights;这是作者最近开发的一种方法，试图使RNA-Seq读取更均匀地分布在表达的转录本上。o makeGeneRepresentation已添加并公开。该函数基于注释计算常量表达式的联合、联合交叉、背景和区域。o validAnnotation现在是公共的。o“使用ShortRead包”小插图的初始重写，其中将包含来自yeastRNASeq包的完全可行的数据分析。o NEWS文件现在可以通过R函数调用NEWS (package = "Genominator")进行解析。o更改importFromAlignedReads只有一个参数“x”，而不是“alignedReads”和“文件名”。o为importFromAlignedReads添加了功能，这样就可以立即将几个文件合并在一起，代价是将它们同时保存在内存中(稍后可能会更改)。 o Added groupBy to summarizeByAnnotation. o Added to Bioconductor. o Improved User Guide substantially o Added CITATION file. BUG FIXES o Fixed a bug related to the deprecation of IRanges::matchMatrix. o Fixed two bugs discovered by Elizabeth Purdom regarding wrong indexing in .writeRegionsTable and importToExpData. o Changed some internals of the plotting functionality to make it work with a GenomeGraphs update. o The new version of DBI (0.2-5) fixes the name mangling of the SQL reserved keyword "end". Workarounds for this mangling has been removed and Genominator now depends on DBI >= 0.2-5. o Added a check to importToExpData so that only rows with non-missing values of (chr, location, strand) gets written to the database. o Fixed the connection pool to be outside of individual ExpData objects. This elucidated a hitherto unknown bug where a user could inadvertently write to a read-only database. o (Internal) Changed a few tryCatch statements to use the SQL "... IF EXISTS ..." instead. o Changed the db and filename to be in sync: there is now only a dbFIlename slot in ExpData and all functions accept dbFilename. CHANGES IN GENOMINATOR VERSION 1.0 NEW FEATURES o Changed underlying database model where now the database exists in two modes, either a read or write mode. This should be somewhat transparent to the end user. o Added importFromAlignedRead which allows the importing of objects read using readAligned from ShortRead package. o Added support for arbitrary index columns, this support allows for the inclusion of more complex types of reads, e.g. reads of different lengths or paired end reads. This support is preliminary, but should allow for a mix of representations. o Added '$' and '[' methods to expData objects to directly query the database. o Fixed vignette to more correctly describe splitByAnnotation. o Added ability to filter the reads when importing an Eland export file. o Added whereClause to summarizeExpData. o Added sample = FALSE argument to plot function for goodness of fit plots. This allows one to plot fewer than all of the points for smaller pdfs. o Added regionGoodnessOfFit.df to work with matrices or data.frames. o Added in-memory ordering to importToExpData; this speeds things up considerably when indexing. BUG FIXES o Fixed bug where colnames are trashed when preserveColnames = T and bindAnno = T o Modified fix below when we include "what" argument. o Fixed bug in splitByAnnotation when expand = TRUE and addOverStrands = TRUE and only one strand was present in the sequencing reads. o Fixed bug in splitByAnnotation when expand = TRUE where reads were lost. %%%% Local Variables: %%%% mode: change-log %%%% coding: utf-8 %%%% End: